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A Librarian’s Guide to NCBI: Course Follow-up

NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented A Librarian’s Guide to NCBI. This new course was designed to prepare health science librarians for supporting and training patrons about NCBI molecular databases and tools at their own institutions.

Participants, instructors, and organizers in the first offering of “A Librarian’s Guide to NCBI” outside the National Library of Medicine.

We have made all of the course materials available. Feel free to learn from these, adapt them for your own teaching, or share them with others. You can use the links below access the course materials, which include the slide sets with quizzes, demonstrations and practice problems, or visit the FTP site to get all the materials.

Sample slides from the eight modules of A Librarian’s Guide to NCBI. Complete PowerPoint files are available from the FTP site.

For a review of molecular biology concepts focusing on biological information flow and the gene as a central theme and Gene as central NCBI see the introductory Molecular Biology Basics materials.

Get the Advanced Entrez Searching module to learn how to use the Entrez integrated database and search system to find relevant data using basic and advanced interfaces, fielded searches and pre-compiled and pre-computed relationships.

You can gain practical experience and a theoretical understanding of NCBI’s sequence similarity search tool BLAST through the Guide to NCBI BLAST, which covers the basics of sequence alignment algorithms, scoring matrices, and local alignment statistics. It also uses practical protein and nucleotide search examples that highlight features of the BLAST web service designed to give the most relevant results.

Learn about the essential role of nucleotide and protein sequence data in modern biological research and about NCBI sequence databases through the Sequences & Genomes materials. You can also find out about the scope, purpose and content of the Assembly, BioProject, and Genome databases, how the NCBI manages and processes sequence and other data associated with genomes and their annotation, and how to find the most up-to-date and well-annotated sequences at the NCBI.

Survey the many databases and tools at NCBI that provide access to variation data through the Sequence Variation and its Consequences materials. These materials cover the Gene, dbSNP, dbGaP, dbVar, and PheGenI resources with an emphasis on the association between variation and disease risk. You can learn about the different types of genetic variation and the major project types that produce these data, as well as how to navigate the NCBI variation resources to find specific data and important attributes, such as geographic population, allele frequency, and disease association.

Get the Gene Expression & Biological Pathways course materials to explore NCBI databases and tools relevant to the study of gene expression, including Gene Expression Omnibus resources (Datasets, Profiles and the GEO2R comparison tool), UniGene, and biological pathways in BioSystems. You can learn the about the importance of gene expression in various biological phenomena, large-scale techniques (microarray, RNAseq) for measuring expression as well as how to find and compare expression patterns of genes in microarray datasets in GEO and in UniGene and how to map selected genes onto metabolic pathways in BioSystems.

Explore the NCBI protein structure databases and tools including the Entrez Structure and Conserved Domains databases and the structure viewer, Cn3D with the Protein Structures module. You can navigate across these resources, learn basic concepts of structural biology and the importance of 3D structural information in understanding the normal functions of proteins and abnormal functions that result in disease, all using DNA topoisomerase as an example. You can also learn how to find available 3D structural data for a given protein sequence, how to detect functional domains within the sequence, how to view the 3D structural data in Cn3D and to compare a protein query protein sequence to the structural data.

Discover NCBI’s Chemical and Bioactivity Databases, which are the part of the PubChem resource, through the Drugs & Other Small Molecules materials. Find out about PubChem databases (Compound, Substance and BioAssay), the types of data that are accessible from these resources, and understand how to find and use this information to answer important scientific questions.

The Librarian’s Guide Exercises page lists the practice problems that are part of the modules and links to an interface that serves as a stepwise guide to the practice problems.

We plan to expand the course materials to include a set of videos of the lectures and demonstrations to be produced for the NCBI YouTube channel as well as a set of worked exercises suitable for classroom teaching. Expanded materials will be available on the NCBI Education page in the near future.

We will offer the Librarian’s Guide at least once a year. Check back on NCBI’s Education page for future offerings of this and other NCBI courses.